Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Attributes | List of all members
protocols::frag_picker::BoundedCollector< StrictWeakOrdering > Class Template Reference

Keeps the N best fragments candidates for the final selection. More...

#include <BoundedCollector.hh>

Public Types

typedef
utility::pointer::owning_ptr
< BoundedCollector
< StrictWeakOrdering > > 
BoundedCollectorOP
 
typedef
utility::pointer::owning_ptr
< BoundedCollector
< StrictWeakOrdering > const > 
BoundedCollectorCOP
 

Public Member Functions

 BoundedCollector (Size query_size, Size max_frags_per_pos, StrictWeakOrdering fragment_comparator, Size n_score_terms, Size buffer_factor=5)
 create a collector for a given size of a query sequence More...
 
bool add (ScoredCandidate new_canditate)
 Insert a fragment candidate to the container. More...
 
Size count_candidates (Size seq_pos) const
 Check how many candidates have been already collected for a given position APL Note: you cannot have inlined virtual functions. More...
 
Size count_candidates () const
 Check how many candidates have been already collected for all positions APL Note: you cannot have inlined virtual functions. More...
 
Size query_length () const
 Check the size of query sequence that this object knows. This is mainly to be able to check if it is the same as in the other parts of fragment picking machinery. More...
 
void insert (Size pos, CandidatesCollectorOP collector)
 Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate. More...
 
ScoredCandidatesVector1get_candidates (Size position_in_query)
 returns all stored fragment candidates that begins at a given position in a query More...
 
void clear ()
 removes all candidates from the container More...
 
void print_report (std::ostream &out, scores::FragmentScoreManagerOP scoring) const
 prints how many candidates have been collected for each position and how good they are More...
 

Private Attributes

utility::vector1
< LazySortedVector1< std::pair
< FragmentCandidateOP,
scores::FragmentScoreMapOP >
, StrictWeakOrdering > > 
storage_
 

Detailed Description

template<class StrictWeakOrdering>
class protocols::frag_picker::BoundedCollector< StrictWeakOrdering >

Keeps the N best fragments candidates for the final selection.

Detailed: The purpose of a collector is to keep the best fragment candidates to the end
of vall processing. In particular, the capacity of this collector may be larger than the number of fragments one wants to get

Member Typedef Documentation

template<class StrictWeakOrdering>
typedef utility::pointer::owning_ptr< BoundedCollector< StrictWeakOrdering > const> protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::BoundedCollectorCOP
template<class StrictWeakOrdering>
typedef utility::pointer::owning_ptr< BoundedCollector< StrictWeakOrdering > > protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::BoundedCollectorOP

Constructor & Destructor Documentation

template<class StrictWeakOrdering>
protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::BoundedCollector ( Size  query_size,
Size  max_frags_per_pos,
StrictWeakOrdering  fragment_comparator,
Size  n_score_terms,
Size  buffer_factor = 5 
)
inline

create a collector for a given size of a query sequence

Member Function Documentation

template<class StrictWeakOrdering>
bool protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::add ( ScoredCandidate  new_canditate)
inlinevirtual

Insert a fragment candidate to the container.

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>
void protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::clear ( )
inlinevirtual
template<class StrictWeakOrdering>
Size protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::count_candidates ( Size  seq_pos) const
inlinevirtual

Check how many candidates have been already collected for a given position APL Note: you cannot have inlined virtual functions.

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>
Size protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::count_candidates ( ) const
inlinevirtual

Check how many candidates have been already collected for all positions APL Note: you cannot have inlined virtual functions.

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>
ScoredCandidatesVector1& protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::get_candidates ( Size  position_in_query)
inlinevirtual

returns all stored fragment candidates that begins at a given position in a query

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>
void protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::insert ( Size  pos,
CandidatesCollectorOP  collector 
)
inlinevirtual

Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate.

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>
void protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::print_report ( std::ostream &  out,
scores::FragmentScoreManagerOP  scoring 
) const
inlinevirtual

prints how many candidates have been collected for each position and how good they are

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>
Size protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::query_length ( ) const
inlinevirtual

Check the size of query sequence that this object knows. This is mainly to be able to check if it is the same as in the other parts of fragment picking machinery.

Implements protocols::frag_picker::CandidatesCollector.

Member Data Documentation

template<class StrictWeakOrdering>
utility::vector1< LazySortedVector1< std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP> , StrictWeakOrdering> > protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::storage_
private

The documentation for this class was generated from the following files: